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Pattern Programming Introduction to Seeds Framework

Pattern Programming Introduction to Seeds Framework. ITCS 4/5145 Parallel Programming Spring 2013 PatterrnProgIntro.ppt Modification date: April 15, 2013. 1. Problem Addressed. To make parallel programming more useable and scalable.

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Pattern Programming Introduction to Seeds Framework

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  1. Pattern Programming Introduction to Seeds Framework ITCS 4/5145 Parallel Programming Spring 2013 PatterrnProgIntro.ppt Modification date: April 15, 2013 1

  2. Problem Addressed • To make parallel programming more useable and scalable. • Parallel programming -- writing programs using multiple computers and processors collectively to solve problems -- has a very long history but still a challenge. 2

  3. Traditional approach • Traditional approach • Explicitly specifying message-passing (MPI), and • Low-level threads APIs (Pthreads, Java threads, OpenMP, …). • Need a better structured approach. 3

  4. Pattern Programming Concept Programmer begins by constructing his program using established computational or algorithmic “patterns” that provide a structure. “Design patterns” part of software engineering for many years: • Reusable solutions to commonly occurring problems * • Patterns provide guide to “best practices”, not a final implementation • Provides good scalable design structure • Can reason more easier about programs • Potential for automatic conversion into executable code avoiding low-level programming – We do that here. • Particularly useful for the complexities of parallel/distributed computing * http://en.wikipedia.org/wiki/Design_pattern_(computer_science)

  5. In Parallel/Distributed computing What patterns are we talking about? • Low-level algorithmic patterns that might be embedded into a program such as fork-join, broadcast/scatter/gather. • Higher level algorithm patterns for forming a complete program such as workpool, pipeline, stencil, map-reduce. We concentrate upon higher-level “computational/algorithm ” level patterns rather than lower level patterns.

  6. Some Patterns Workpool Workers Two-way connection Master Compute node Source/sink

  7. Pipeline Stage 1 Stage 2 Stage 3 Workers One-way connection Two-way connection Master Compute node Source/sink

  8. Divide and Conquer Two-way connection Divide Merge Compute node Source/sink

  9. All-to-All Two-way connection Compute node Source/sink

  10. Usually a synchronous computation - Performs number of iterations to converge on solution e.g. for solving Laplace’s/heat equation Stencil On each iteration, each node communicates with neighbors to get stored computed values Two-way connection Compute node Source/sink

  11. Parallel Patterns • Advantages • Possible to create parallel code from the pattern specification automatically – see later. • Abstracts/hides underlying computing environment • Generally avoids deadlocks and race conditions • Reduces source code size (lines of code) • Hierarchical designs with patterns embedded into patterns, and pattern operators to combine patterns • Disadvantages • New approach to learn • Takes away some of the freedom from programmer • Performance reduced slightly(but compare using high level languages instead of assembly language)

  12. Previous/Existing Work • Patterns explored in several projects. • Industrial efforts • Intel Threading Building Blocks (TBB), Intel Cilk plus, Intel Array Building Blocks (ArBB). Focus on very low level patterns such as fork-join • Universities: • University of Illinois at Urbana-Champaign and University of California, Berkeley • University of Torino/Università di Pisa Italy

  13. Our approach Focuses on a few higher level patterns of wide applicability (e.g. workpool, synchronous all-to-all, pipelined, stencil). Software framework developed called “Seeds” to easily construct an application from established patterns without need to write low level message passing or thread based code. Will to automatically distribute code across processor cores, computers, or geographical distributed computers and execute the parallel code.

  14. Pattern Programmingwith the Seeds Framework

  15. Basic User Programmer Interface To create and execute parallel programs, programmer selects a pattern and implements three principal Java methods with a module class: • Diffuse method – to distribute pieces of data. • Compute method – the actual computation • Gather method – used to gather the results Programmer also has to fill in details in a “bootstrap” class to deploy and start the framework. “Module” class Diffuse Compute Gather “Run module” bootstrap class The framework self-deploys on a geographically distributed platform and executes pattern.

  16. Module class segment used by Framework to keep track of where to put results Data cast into a DataMap By framework public Data DiffuseData (int segment) { DataMap<String, Object> d =new DataMap<String, Object>(); input Data = …. d.put(“name_of_inputdata", inputData); return d; } public Data Compute (Data data) { DataMap<String, Object> input = (DataMap<String,Object>)data; //data produced by DiffuseData() DataMap<String, Object> output = new DataMap<String, Object>(); //output returned to gatherdata inputData = input.get(“name_of_inputdata”); … // computation output.put("name_of _results", results); // to return to GatherData() return output; } public void GatherData (int segment, Data dat) { DataMap<String,Object> out = (DataMap<String,Object>) dat; outdata = out.get (“name_of_results”); result … // aggregate outdata from all the worker nodes. result a private variable } GatherData gives back Data object with a segment number By framework

  17. Seeds WorkpoolDiffuseData, Compute, and GatherData Methods GatherData DiffuseData Private variable total (answer) DataMap d Master Returns d to each slave Compute Note DiffuseData, Compute and GatherData methods start with a capital letter although method names should not! DataMap input Slaves DataMap output DataMap d created in diffuse DataMap output created in compute

  18. Data and DataMap classes For implementation convenience two classes: • Data class used to pass data between master and slaves Uses a “segment” number to keep track of packets as they go from one method to another. • DataMap class inside compute method DataMap is a subclass of Data and so allows casting. DataMap methods • put (String, data) – puts data into DataMap identified by string • get (String) – gets stored data identified by string DataMap extends Java HashMap which implement a Map, see http://doc.java.sun.com/DocWeb/api/java.util.HashMap

  19. Seeds Implementations • JXTA P2P networking version suitable for a fully distributed network of computers and requiring an Internet connection even in just running on a single computer, • “No Network” JXTA P2P version for running on a single computer, not requiring an Internet connection • Multicore version implemented with threads for more efficient execution on single multicore computer or shared memory multiprocessor system -- does not require an Internet connection. • Two JXTA versions use the same application code and run in a similar fashion • Multicore version use same Module code but slightly Bootstrap Run Module source code (see next)

  20. Bootstrap classJXTA P2P version This code deploys framework and starts execution of pattern package edu.uncc.grid.example.workpool; import java.io.IOException; import net.jxta.pipe.PipeID; import edu.uncc.grid.pgaf.Anchor; import edu.uncc.grid.pgaf.Operand; import edu.uncc.grid.pgaf.Seeds; import edu.uncc.grid.pgaf.p2p.Types; public class RunMonteCarloPiModule { public static void main(String[] args) { try { MyModule pi = new MyModule(); Seeds.start( "/path/to/seeds/seed/folder" , false); // starts framework, deploy on list of servers PipeID id = Seeds.startPattern(new Operand( (String[])null, new Anchor( "hostname" , Types.DataFlowRoll.SINK_SOURCE), pi ) ); // starts seeds pattern System.out.println(id.toString() ); Seeds.waitOnPattern(id); // waits for pattern to complete System.out.println( "The result is: " + pi.getPi() ) ; Seeds.stop(); //stop framework } catch (SecurityException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } catch (Exception e) { e.printStackTrace(); } } } Name of module class Different patterns have similar code

  21. Bootstrap classMulticore version public class RunMonteCarloPiModule { public static void main(String[] args) { try { MyModule pi=new MyiModule(); Thread id = Seeds.startPatternMulticore( new Operand( (String[])null , new Anchor( args[0], Types.DataFlowRole.SINK_SOURCE) , pi ), 4 ); id.join(); System.out.println( "The result is: " + pi.getPi() ) ; } catch (SecurityException e) { … } } } • Thread-based version using shared memory • Faster than JXTA P2P version on a multicore platform • Bootstrap class does not need to start/stop JXTA P2P. Seeds.start() and Seeds.stop() not needed. • Module class unchanged

  22. Measuring Time Can instrument code in the bootstrap class: public class RunMyModule { public static void main (String [] args ) { try{ long start = System.currentTimeMillis(); MyModule m = new MyModule(); Seeds.start(. ); PipeID id = ( … ); Seeds.waitOnPattern(id); Seeds.stop(); long stop = System.currentTimeMillis(); double time = (double) (stop - start) / 1000.0; System.out.println(“Execution time = " + time); } catch (SecurityException e) { … …

  23. Compiling/executing • Can be done on the command line (ant script provided) or through an IDE (Eclipse)

  24. Pattern Programmingwith the Seeds FrameworkWorkpool patternMatrix addition and multiplication

  25. Matrix Addition, C = A + B Add corresponding elements of each matrix to form elements of result matrix. Given elements of A as ai,jand elements of B as bi,j, each element of C computed as: Add A B C Easy to parallelize – each processor computes one C element or group of C elements

  26. Workpool Implementation Slave computation Adds one row of A with one row of B to create one row of C (rather than each slave adding single elements) Add A B C

  27. Workpool implementation Slaves (one for each row) Return one row of C C A B Send one row of A and B to slave Master Compute node Source/sink Following example 3 x 3 arrays and 3 slaves

  28. MatrixAddModule.javaContinues on several sides package edu.uncc.grid.example.workpool; import … public class MatrixAddModule extends Workpool { private static final long serialVersionUID = 1L; int[][] matrixA; int[][] matrixB; int[][] matrixC; public MatrixAddModule() { matrixC = new int[3][3]; } public void initMatrices(){ matrixA = new int[][]{{2,5,8},{3,4,9},{1,5,2}}; matrixB = new int[][]{{2,5,8},{3,4,9},{1,5,2}}; } public intgetDataCount() { return 3; } public void initializeModule(String[] args) { Node.getLog().setLevel(Level.WARNING); } In this example matrices are 3 x 3 Some initial values Required method. Number of data objects (Slaves)

  29. DiffuseData method DataMap d returned are pairs of string key and associated array public Data DiffuseData(int segment) { int[] rowA = new int[3]; int[] rowB = new int[3]; DataMap<String, int[]> d =new DataMap<String, int[]>(); int k = segment; for (inti=0;i<3;i++) { rowA[i] = matrixA[k][i]; rowB[i] = matrixB[k][i]; } d.put("rowA",rowA); d.put("rowB",rowB); return d; } segment variable used to select rows Copy one row of A and one row of B into rowA, rowB to be sent to slaves rowA and rowB put in d DataMap to send to slaves

  30. Compute method public Data Compute(Data data) { int[] rowC = new int[3]; DataMap<String, int[]> input = (DataMap<String,int[]>)data; DataMap<String, int[]> output = new DataMap<String, int[]>(); int[] rowA = (int[]) input.get("rowA"); int[] rowB = (int[]) input.get("rowB"); for (inti=0;i<3;i++) { rowC[i] = rowA[i] + rowB[i]; } output.put("rowC",rowC); return output; } Get two rows from data received Add rows Put result row into output with key to be sent back to master

  31. GatherData method Note segment variable and Data from slave public void GatherData(int segment, Data dat) { DataMap<String,int[]> out = (DataMap<String,int[]>) dat; int[] rowC = (int[]) out.get("rowC"); for (inti=0;i<3;i++) { matrixC[segment][i]= rowC[i]; } } Get C row sent from slave Place row into result matrix Segment variable associated with Data used to choose correct row

  32. Bootstrap class - RunMatrixAddModule.java package edu.uncc.grid.example.workpool; import … public class RunMatrixAddModule { public static void main (String [] args ) { try { long start = System.currentTimeMillis(); Seeds.start( args[0] ,false); MatrixAddModule m = new MatrixAddModule(); m.initMatrices(); PipeID id = Seeds.startPattern(new Operand ((String[])null,new Anchor (args[1], Types.DataFlowRoll.SINK_SOURCE),m)); Seeds.waitOnPattern(id); m.printResult(); Seeds.stop(); long stop = System.currentTimeMillis(); double time = (double) (stop - start) / 1000.0; System.out.println("Execution time = " + time); … In this example the path to Seeds and local host name are command line arguments

  33. Matrix Multiplication, C = A * B One slave computes one element of result in workpool implementation

  34. Workpool implementation Slaves (one for each element of result) Return one element of C C A Send one row of A and one column of B to slave B Master Compute node Following example 3 x 3 arrays and 9 slaves Source/sink

  35. MatrixAddModule.javaContinues on several sides package edu.uncc.grid.example.workpool; import … public class MatrixAddModule extends Workpool { private static final long serialVersionUID = 1L; int[][] matrixA; int[][] matrixB; int[][] matrixC; public MatrixAddModule() { matrixC = new int[3][3]; } public void initMatrices(){ matrixA = new int[][]{{2,5,8},{3,4,9},{1,5,2}}; matrixB = new int[][]{{2,5,8},{3,4,9},{1,5,2}}; } public intgetDataCount() { return 9; } public void initializeModule(String[] args) { Node.getLog().setLevel(Level.WARNING); } In this example matrices are 3 x 3 Some initial values Required method. Number of data objects (Slaves)

  36. Note on mapping rows and columns to segments Arow Bcol segment 0 0 0 segment 1 0 1 segment 2 0 2 segment 3 1 0 segment 4 1 1 segment 5 1 2 segment 6 2 0 segment 7 2 1 segment 8 2 2 int Arow =segment/3; Int Bcol segment%3;

  37. DiffuseData method DataMap d returned are pairs of string key and associated array public Data DiffuseData(int segment) { int[] rowA = new int[3]; int[] colB = new int[3]; DataMap<String, int[]> d =new DataMap<String, int[]>(); int a=segment/3,b = segment%3 ; for (inti=0;i<3;i++) { rowA[i] = matrixA[a][i]; colB[i] = matrixB[i][b]; } d.put("rowA",rowA); d.put(“colB",colB); return d; } segment variable used to select element in A and B Copy one row of A and one column of B into rowA, colB to be sent to slaves rowA and colB put in d DataMap to send to slaves

  38. Compute method public Data Compute(Data data) { int[] rowC = new int[3]; DataMap<String, int[]> input = (DataMap<String,int[]>)data; DataMap<String, Integer> output = new DataMap<String, Integer>(); int[] rowA = (int[]) input.get("rowA"); int[] colB = (int[]) input.get(“colB"); int out = 0; for (inti=0;i<3;i++) { out += rowA[i]*colB[i]; } output.put(“out",out); return output; } Get two rows from data received Matrix multiplication, one result Put result into output with key to be sent back to master

  39. GatherData method Note segment variable and Data from slave public void GatherData(int segment, Data dat) { DataMap<String,Integer> out = (DataMap<String,Integer>) dat; int answer = out.get("out"); int a=segment/3, b=segment%3; matrixC[a][b]= answer; } Get result sent from slave* Place element into result matrix Segment variable associated with Data used to choose correct row * Cast from Integer to int not necessary

  40. Bootstrap class - RunMatrixMultiplyModule.javaJXTA P2P version package edu.uncc.grid.example.workpool; import … public class RunMatrixMultiplyModule { public static String localhost = "T5400"; // name of local machine public static String seedslocation = "C:\\seeds_2.0\\pgaf"; public static void main (String [] args ) { try { long start = System.currentTimeMillis(); Seeds.start( seedslocation ,false); MatrixMultiplyModule m = new MatrixMultiplyModule(); m.initMatrices(); PipeID id = Seeds.startPattern(new Operand ((String[])null,new Anchor (localhost, Types.DataFlowRoll.SINK_SOURCE),m)); Seeds.waitOnPattern(id); m.printResult(); Seeds.stop(); long stop = System.currentTimeMillis(); double time = (double) (stop - start) / 1000.0; System.out.println("Execution time = " + time); … In this example, local host and path to Seeds are hardcoded.

  41. Acknowledgements Work initiated by Jeremy Villalobos in his PhD thesis “Running Parallel Applications on a Heterogeneous Environment with Accessible Development Practices and Automatic Scalability,” UNC-Charlotte, 2011. Jeremy developed “Seeds” pattern programming software. Extending work to teaching environment supported by the National Science Foundation under grant "Collaborative Research: Teaching Multicore and Many-Core Programming at a Higher Level of Abstraction" #1141005/1141006 (2012-2015). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.

  42. Department of Computer Science • Pattern Programming Group • http://coitweb.uncc.edu/~abw/PatternProgGroup/Please contact B. Wilkinson if you would like to be involved in this work for academic credit: • Undergraduate senior project/capstone project (ITCS 4650/51/81/82, ITCS 4990/91) • Graduate level ITCS 6880 Individual Study • MS thesis (ITCS 6991) • (Currently no student funding available.)

  43. Questions

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